Yes, i work with scroll lock enabled but key codes for Alt/RAlt & Ctrl/LCtrl (maybe for Shift/LShift too) is similar. My configuration: viewer on Win2k, server on Win7 SP1 x64 (with x64 version of UltraVNC), UltraVNC version - 1.2.1.0.Also i set nohotkeys option to 1 in viewers ini file because i use many hotkeys for macroses. I use a lot FAR manager and for example Ctrl+1 and LCltrl+1 make different operations.

1. Download and run any version of FAR on UVNC server machine (http://farmanager.com/download.php?l=en)2. LCtrl+0..9 - set panel mode3. RCtrl+0..9 - folders shortcuts (but they don't work because RCtrl don't sent by viewer)

I did not find "Alternate keyboard method" in viewer (or viewers ini) but it presentin <Admin Properties> of server. When i turn it on, nothing changes, so i turn it off and try to scan key codes when Scroll Lock is off and it helps. So, if Scroll Lock is off RAlt & RCtrl works fine but turning on/off ScrLk not comfortable in use. Maybe with this information it will be easier to fix?